[MINC-users] Variations on normalization of minc volumes in minc-toolkit

[Alex Zijdenbos]

Just to follow up on Andrew J's explanation: Yes inormalize predates
minccalc by quite a few years :-) It's now somewhat obsolete though. I
actually started writing a perl wrapper around minccalc that
reproduces the functionality of inormalize. It currently is missing a
few of inormalize's options though, but it will hopefully become a
drop-in replacement.nyul

normalize_mri is indeed a wrapper around inormalize, which plays some
tricks by generating masks that may help with volume-to-volume
normalization. By the way inormalize can also do volume-to-constant
normalization, which only requires one input volume.

volume_pol and minc_nuyl both seem to be part of minc-toolkit - I bet
Vladimir can speak to these?

-- A

On Tue, Nov 18, 2014 at 7:03 PM, Andrew Janke <a.janke at gmail.com> wrote:
> Hi Gabriel,
>
> I'll comment on the one I know.
>
> inormalize was written by Alex Z and yes it does require volumes to be
> aligned to a model. There are a few different ways it can be used to
> calculate the map between the two volumes (or even between slices
> within one file). These are detailed in the "Solution options" section
> of inormalize -help.
>
> I tend to use it like this (I've simplified a bit):
>
>       # calculate normalisation
>       map="map.txt"
>       if [ ! -e $map ]
>       then
>          inormalize \
>             -nonormalize -print -quiet \
>             -model model.mnc \
>             -mask model_mask.mnc \
>             $infile |\
>             sed -e 's/^\ \ //' -e 's/(//' -e 's/\,//' -e 's/)//' |\
>             tee $map
>       fi
>
>       # apply it
>       scale=$(grep medianOfRatios $map | cut -f2 -d\ )
>       offset=$(grep medianOfRatios $map | cut -f3 -d\ )
>       minccalc -clobber \
>          -expression "$offset + $scale*A[0]" \
>          $infile $outfile
>
>
> Note that I separate out the calculation and the subsequent
> application of the normalization via minccalc, at the time inormalize
> was written I don't think minccalc existed so I doubt you'll find this
> method in any of the examples!
>
>
> a
>
>
> On 19 November 2014 05:49, Gabriel A. Devenyi <gdevenyi at gmail.com> wrote:
>> Hi All,
>>
>> I'm working on streamlining a
>> parallel grid-aware
>> preprocessing pipeline using bpipe (see https://code.google.com/p/bpipe/
>> and https://github.com/CobraLab/bpipe-library) and I've come across these
>> normalization tools within minc-toolkit:
>>
>> minc_nuyl - documented at http://www.ncbi.nlm.nih.gov/pubmed/10784285
>> volume_pol - no documentation?
>> inormalize - no documentation?
>> normalize_mri - wrapper for inormalize
>>
>> Is there any documentation out there regarding these tools (what they do,
>> and how they do it).
>>
>> Additionally, are there any details on the requirements to apply these
>> tools?
>>
>> For example, the source header in inormalize.cc I think indicates that the
>> volumes must be registered, is that correct?
>>
>>
>> Can anyone provide any insights on these tools? Thanks!
>>
>>
>> --
>> Gabriel A. Devenyi B.Eng. Ph.D.
>> Research Computing Associate
>> Computational Brain Anatomy Laboratory
>> Cerebral Imaging Center
>> Douglas Mental Health University Institute
>> McGill University
>> t: 514.761.6131x4781
>> e: gdevenyi at gmail.com
>> _______________________________________________
>> MINC-users at bic.mni.mcgill.ca
>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
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